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ExtractMMPBSATotals.py
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ExtractMMPBSATotals.py
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# Copyright (c) 2015 William Lees
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
# documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
# persons to whom the Software is furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
# Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
# WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
import sys
import csv
import argparse
from MMPBSA_mods import API as MMPBSA_API
def main(argv):
parser = argparse.ArgumentParser(description='Extract frame-by-frame MMPSA/MMGBSA Energy Totals')
parser.add_argument('outfile', help='output file (CSV)')
parser.add_argument('calc', help='gb (for GBSA) or pb (for PBSA)')
parser.add_argument('-p', '--prefix', help='prefix for MMPBSA files (default _MMPBSA_)')
args = parser.parse_args()
if args.calc not in ['gb', 'pb']:
print 'calc must be either "gb" or "pb"'
quit()
prefix = '_MMPBSA_' if args.prefix is None else args.prefix
data=MMPBSA_API.load_mmpbsa_info(prefix + 'info')
head = ['TOTAL']
with open(args.outfile, 'w') as csvfile:
writer = csv.DictWriter(csvfile, fieldnames=head)
writer.writeheader()
tot = 0
count = 0
for i in range(len(data[args.calc]['complex']['EEL'])):
row = {}
row['TOTAL'] = data[args.calc]['complex']['TOTAL'][i] - data[args.calc]['ligand']['TOTAL'][i] -data[args.calc]['receptor']['TOTAL'][i]
writer.writerow(row)
tot += row['TOTAL']
count += 1
print "%d frames in total. Mean %f." % (count, tot/count)
if __name__ == "__main__":
main(sys.argv)